The idea of the extended phenotype (EP), which was first proposed by the British evolutionary biologist Richard Dawkins to explain how and why organisms—or, more fundamentally, their genes—are able to manipulate their environment (Dawkins, 1982), has been the focus of intense debate and much research for more than 20 years. In his book, The Extended Phenotype: The Long Reach of the Gene, Dawkins observed that, "[the extended phenotype] so far changes the way we see animals and plants that it may cause us to think of testable hypotheses that we would otherwise never have dreamed of." The EP has certainly been the stimulus for a great deal of research activity recently, as the tools of genomics and proteomics provide fresh evidence of its importance. The concept of the EP helps, for example, to explain how parasites modify the behaviour of their hosts to their advantage, or nest-building behaviour in birds. In particular, the relationship between the bacterial flora of the gut and their mammalian hosts has been a hot topic of late; one that has yielded new examples of the EP to support the themes Dawkins originally outlined.

The [extended phenotype] has certainly been the stimulus for a great deal of research activity recently, as the tools of genomics and proteomics provide fresh evidence of its importance

At the same time there has been an ongoing debate among proponents of neo-Darwinism—of which the EP is an important component—between those who advocate the EP and those who advocate theories such as niche construction, which propose that other factors—in addition to genes—have a crucial role in the way that organisms manipulate their environment, so that their descendents inherit both their genetic legacy and their environmental legacy. These different strands of the EP debate were finally pulled together at a conference on the subject, organized by the European Science Foundation (ESF; Strasbourg, France) in late 2008. The main conclusion of the meeting was that the EP concept has become even more relevant in the light of recent research, but that its role will ultimately be restricted to an explanatory one, rather than as a tool for designing meaningful experiments.

In detail, the EP states that the genes of an organism can be expressed beyond their immediate biological boundaries, such as skin, shells or leaves. The EP can embrace nest-building or the manipulation of host behaviour by parasites. The main point is that the EP embraces entities such as nests or the dams built by beavers, the quality or functionality of which is correlated with certain alleles of the organism, on which natural selection can then act. This is the distinction between the EP and niche construction; for example, the EP is subject to a reproductive bottleneck as the benefit of the EP is passed on solely through the genes of an organism, rather than as an altered environmental niche for its progeny. In this manner, an allele that leads to better dams, for example, will increase the fitness of the beaver in which the allele is expressed. Similarly, an allele in a parasite that makes the parasite more effective at weakening the resistance of its host, or that is in some way able to modify its host's behaviour to make it more likely that the parasite's progeny will find a new host, will similarly be selected for by natural selection.

As Dawkins wrote, "Replicators are not, of course, selected directly, but by proxy; they are judged by their phenotypic effects. Although for some purposes it is convenient to think of these phenotypic effects as being packaged together in discrete 'vehicles' such as individual organisms, this is not fundamentally necessary. Rather, the replicator should be thought of as having extended phenotypic effects, consisting of all its effects on the world at large, not just its effects on the individual body in which it happens to be sitting" (Dawkins, 1982).